ArticleNature communications2023
Streamlined structure determination by cryo-electron tomography and subtomogram averaging using TomoBEAR.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 46 citations in OpenAlex.
- Ligand-induced activation of RyR1 in native membranes.Nature communications · 2026Article
- Structures of EHD2 filaments on curved membranes provide a model for caveolar neck stabilization.Nature communications · 2026Article
- FlyTomo: a streamlined software for on-the-fly cryo-ET data processing and diagnosis.Nature communications · 2026Article
- AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time and at high throughput.Nature methods · 2026Article
- In situ structure determination of conformationally flexible targets using nextPYP.Nature protocols · 2026Review
- Structural Analysis of Membrane Proteins in Cell-Derived Microvesicles.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Dynamic nanoscale architecture of synaptic vesicle fusion in mouse hippocampal neurons.Nature communications · 2025Article
- Strategies for studying discrete heterogeneity in situ using cryo-electron tomography.Current opinion in structural biology · 2025Review
- A practical look at cryo-electron tomography image processing: Key considerations for new biological discoveries.Current opinion in structural biology · 2025Review
- Structural insights into GPCR signaling activated by peptide ligands: from molecular mechanism to therapeutic application.Experimental & molecular medicine · 2025Review
- pytom-match-pick: A tophat-transform constraint for automated classification in template matching.Journal of structural biology: X · 2025Article
- A case for community metadata standards in cryo-electron tomography.Emerging topics in life sciences · 2025Review
- Unraveling atomic complexity from frozen samples.Structural dynamics (Melville, N.Y.) · 2025Article
- High-resolution protein modeling through Cryo-EM and AI: current trends and future perspectives - a review.Frontiers in molecular biosciences · 2025Review
- Molecular architecture of synaptic vesicles.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Article
- An image processing pipeline for electron cryo-tomography in RELION-5.FEBS open bio · 2024Article
- Structure of tetrameric forms of the serotonin-gated 5-HT3The EMBO journal · 2024Article
- Smart parallel automated cryo-electron tomography.Nature methods · 2024Article
- TOMOMAN: a software package for large scale cryo-electron tomography data preprocessing, community data sharing, and collaborative computing.bioRxiv : the preprint server for biology · 2024Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Structures of macromolecules in their native state provide unique unambiguous insights into their functions. Cryo-electron tomography combined with subtomogram averaging demonstrated the power to solve such structures in situ at resolutions in the range of 3 Angstrom for some macromolecules. In order to be applicable to the structural determination of the majority of macromolecules observable in cells in limited amounts, processing of tomographic data has to be performed in a high-throughput manner. Here we present TomoBEAR-a modular configurable workflow engine for streamlined processing of cryo-electron tomographic data for subtomogram averaging. TomoBEAR combines commonly used cryo-EM packages with reasonable presets to provide a transparent ("white box") approach for data management and processing. We demonstrate applications of TomoBEAR to two data sets of purified macromolecular targets, to an ion channel RyR1 in a membrane, and the tomograms of plasma FIB-milled lamellae and demonstrate the ability to produce high-resolution structures. TomoBEAR speeds up data processing, minimizes human interventions, and will help accelerate the adoption of in situ structural biology by cryo-ET. The source code and the documentation are freely available.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.